As an emerging disease, the porcine epidemic diarrhoea virus has caused substantial economic losses to the pork industry in Mexico, leading to piglet mortality rates of up to 100%. For detection, sequencing and genetic characterization of the virus, 68 samples of one-week-old piglets from pork farms in 17 states of Mexico were analysed. In total, 53 samples were positive by real-time RT-PCR, confirming the presence of the virus in 15 states. Twenty-eight samples from 10 states were amplified by endpoint RT-PCR, and 20 sequences of the spike gene were obtained. A phylogenetic analysis based on the spike gene demonstrated that all Mexican strains are in Group II and are classified as non-Indel-S emerging variants. Three strains showed amino acid insertions: PEDv/MEX/GTO/LI-DMZC15/2015 and PEDv/MEX/QRO/LI-DMZC45/2016 showed one amino acid insertion (424 Y425 and 447 D448 , respectively), and PEDv/MEX/QRO/LI-DMZC49/2019 showed one and two amino acid insertions (422 C423 and 537 SQ538 ), with the second insertion in the COE region. These results provide evidence of the prevalence of emerging, non-Indel-S strains of the virus are currently circulating in Mexico during 2016-2018, when three of which have amino acid insertions: PEDv/MEX/GTO/IN-DMZC15/2015 and PEDv/MEX/QRO/IN-DMZC45/2016 have one amino acid insertion each (424 Y425 and 447 D448 , respectively), and PEDv/MEX/QRO/IN-DMZC49/2019 has one (422 C423 ) and two amino acid insertions (537 SQ538 ), the latter being in the COE region, which could generate new antigenic variants.

中文翻译：

---

墨西哥的猪流行性腹泻病毒（PEDv）新兴菌株。

猪流行性腹泻病毒是一种新兴疾病，已经给墨西哥的猪肉业造成了巨大的经济损失，导致仔猪死亡率高达100％。为了对该病毒进行检测，测序和遗传表征，分析了来自墨西哥17个州的养猪场的68个1周龄小猪的样本。总共有53个样品通过实时RT-PCR呈阳性，确认了该病毒在15个州中的存在。通过终点RT-PCR扩增了来自10个州的28个样品，并获得了20个穗基因序列。基于穗基因的系统发育分析表明，所有墨西哥菌株都属于第二类，被归类为非Indel-S新兴变异体。三种菌株显示出氨基酸插入：PEDv / MEX / GTO / LI-DMZC15 / 2015和PEDv / MEX / QRO / LI-DMZC45 / 2016显示一个氨基酸插入（分别为424 Y425和447 D448），以及PEDv / MEX / QRO / LI-DMZC49 / 2019显示了一个和两个氨基酸插入（422 C423和537 SQ538），第二个插入在COE区域。这些结果提供了在2016-2018年期间墨西哥正在流行的新兴非Indel-S病毒株的证据，其中三个具有氨基酸插入序列：PEDv / MEX / GTO / IN-DMZC15 / 2015和PEDv / MEX / QRO / IN-DMZC45 / 2016每个有一个氨基酸插入（分别是424 Y425和447 D448），而PEDv / MEX / QRO / IN-DMZC49 / 2019有一个氨基酸插入（422 C423）和两个氨基酸插入（537 SQ538），后者位于COE区域，可以产生新的抗原变体。和PEDv / MEX / QRO / LI-DMZC49 / 2019显示一个和两个氨基酸插入（422 C423和537 SQ538），第二个插入在COE区域中。这些结果提供了在2016-2018年期间墨西哥正在流行的新兴非Indel-S病毒株的证据，其中三个具有氨基酸插入序列：PEDv / MEX / GTO / IN-DMZC15 / 2015和PEDv / MEX / QRO / IN-DMZC45 / 2016每个都有一个氨基酸插入（分别为424 Y425和447 D448），而PEDv / MEX / QRO / IN-DMZC49 / 2019有一个氨基酸插入（422 C423）和两个氨基酸插入（537 SQ538），后者位于COE区域，可以产生新的抗原变体。和PEDv / MEX / QRO / LI-DMZC49 / 2019显示一个和两个氨基酸插入（422 C423和537 SQ538），第二个插入在COE区域中。这些结果提供了在2016-2018年期间墨西哥正在流行的新兴非Indel-S病毒株的证据，其中三个具有氨基酸插入序列：PEDv / MEX / GTO / IN-DMZC15 / 2015和PEDv / MEX / QRO / IN-DMZC45 / 2016每个有一个氨基酸插入（分别是424 Y425和447 D448），而PEDv / MEX / QRO / IN-DMZC49 / 2019有一个氨基酸插入（422 C423）和两个氨基酸插入（537 SQ538），后者位于COE区域，可以产生新的抗原变体。